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- PDB-5fhz: Human aldehyde dehydrogenase 1A3 complexed with NAD(+) and retino... -

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Basic information

Entry
Database: PDB / ID: 5fhz
TitleHuman aldehyde dehydrogenase 1A3 complexed with NAD(+) and retinoic acid
ComponentsAldehyde dehydrogenase family 1 member A3
KeywordsOXIDOREDUCTASE / Human / retinaldehyde dehydrogenase / tetramer / product-bound structure
Function / homology
Function and homology information


nucleus accumbens development / optic cup morphogenesis involved in camera-type eye development / olfactory pit development / Harderian gland development / retinoic acid biosynthetic process / embryonic eye morphogenesis / retinal dehydrogenase / embryonic camera-type eye development / aldehyde dehydrogenase [NAD(P)+] activity / RA biosynthesis pathway ...nucleus accumbens development / optic cup morphogenesis involved in camera-type eye development / olfactory pit development / Harderian gland development / retinoic acid biosynthetic process / embryonic eye morphogenesis / retinal dehydrogenase / embryonic camera-type eye development / aldehyde dehydrogenase [NAD(P)+] activity / RA biosynthesis pathway / righting reflex / retinal metabolic process / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / retinol metabolic process / retinoic acid metabolic process / inner ear morphogenesis / face development / thyroid hormone binding / neuromuscular process controlling balance / NAD+ binding / locomotory behavior / protein homotetramerization / positive regulation of apoptotic process / apoptotic process / protein homodimerization activity / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RETINOIC ACID / Retinaldehyde dehydrogenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMoretti, A. / Rizzi, M. / Garavaglia, S.
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structure of human aldehyde dehydrogenase 1A3 complexed with NAD(+) and retinoic acid.
Authors: Moretti, A. / Li, J. / Donini, S. / Sobol, R.W. / Rizzi, M. / Garavaglia, S.
History
DepositionDec 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase family 1 member A3
B: Aldehyde dehydrogenase family 1 member A3
C: Aldehyde dehydrogenase family 1 member A3
D: Aldehyde dehydrogenase family 1 member A3
E: Aldehyde dehydrogenase family 1 member A3
F: Aldehyde dehydrogenase family 1 member A3
G: Aldehyde dehydrogenase family 1 member A3
H: Aldehyde dehydrogenase family 1 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,00120
Polymers465,4928
Non-polymers6,50912
Water1,13563
1
A: Aldehyde dehydrogenase family 1 member A3
B: Aldehyde dehydrogenase family 1 member A3
C: Aldehyde dehydrogenase family 1 member A3
D: Aldehyde dehydrogenase family 1 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,60212
Polymers232,7464
Non-polymers3,8558
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25210 Å2
ΔGint-99 kcal/mol
Surface area60800 Å2
MethodPISA
2
E: Aldehyde dehydrogenase family 1 member A3
F: Aldehyde dehydrogenase family 1 member A3
G: Aldehyde dehydrogenase family 1 member A3
H: Aldehyde dehydrogenase family 1 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,4008
Polymers232,7464
Non-polymers2,6544
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22380 Å2
ΔGint-94 kcal/mol
Surface area60940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.656, 159.785, 177.647
Angle α, β, γ (deg.)90.00, 93.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
31B
41C
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 29 - 501 / Label seq-ID: 46 - 518

Dom-IDAuth asym-IDLabel asym-ID
1DD
2AA
3BB
4CC
5EE
6FF
7GG
8HH

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Components

#1: Protein
Aldehyde dehydrogenase family 1 member A3 / Aldehyde dehydrogenase 6 / Retinaldehyde dehydrogenase 3 / RalDH3


Mass: 58186.527 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Missing residues of the crystal structure are due to weak electron density
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1A3, ALDH6 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P47895, aldehyde dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-REA / RETINOIC ACID / Retinoic acid


Mass: 300.435 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H28O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 3350, 0.24 M Na2 malonate pH 7.0, 10 mM TCEP hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.899 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.899 Å / Relative weight: 1
ReflectionResolution: 2.9→49.57 Å / Num. all: 364821 / Num. obs: 100139 / % possible obs: 98.29 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.1822 / Net I/σ(I): 5.35
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.46 / % possible all: 97.44

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
PHASERphasing
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BXS

1bxs


Resolution: 2.9→49.57 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.848 / SU B: 23.02 / SU ML: 0.432 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28923 5047 5 %RANDOM
Rwork0.22808 ---
obs0.23118 95090 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.479 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.02 Å2
2--0.01 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29489 0 440 63 29992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01930556
X-RAY DIFFRACTIONr_bond_other_d0.0020.0229469
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.98441406
X-RAY DIFFRACTIONr_angle_other_deg1.936367995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33453799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53324.4521278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26155229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.81115168
X-RAY DIFFRACTIONr_chiral_restr0.0680.24645
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02134229
X-RAY DIFFRACTIONr_gen_planes_other0.0040.026772
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2794.31115253
X-RAY DIFFRACTIONr_mcbond_other2.2784.31115252
X-RAY DIFFRACTIONr_mcangle_it3.476.45919033
X-RAY DIFFRACTIONr_mcangle_other3.476.45919034
X-RAY DIFFRACTIONr_scbond_it2.854.47815303
X-RAY DIFFRACTIONr_scbond_other2.854.47815304
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1226.63422374
X-RAY DIFFRACTIONr_long_range_B_refined5.20834.24934832
X-RAY DIFFRACTIONr_long_range_B_other5.20834.24934832
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 6402 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.590.5
Bmedium positional0.630.5
Cmedium positional0.740.5
Dmedium positional0.640.5
Emedium positional0.750.5
Fmedium positional0.830.5
Gmedium positional0.740.5
Hmedium positional0.750.5
Amedium thermal19.552
Bmedium thermal19.322
Cmedium thermal18.992
Dmedium thermal17.122
Emedium thermal20.982
Fmedium thermal18.232
Gmedium thermal18.042
Hmedium thermal18.22
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 360 -
Rwork0.326 6942 -
obs--97.63 %

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